7V08: 60S ribosomal protein L2-A

Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state from a Spb1 D52A suppressor 3 strain. Determined by electron microscopy at 2.36 Å resolution. Released 15 Mar 2023.

Method
Electron microscopy
Resolution
2.36 Å
Organism
Saccharomyces cerevisiae BY4741
Chains
60
Atoms
157,839
Mol. weight
2673.43 kDa
Ligands
MG, B3P, ZN, GDP
Released
15 Mar 2023

Explore 7V08 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7V08 contains 568 α-helices and 487 β-strands across 56 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain 4: 27 helices, 28 β-strands

ElementResiduesLengthSheet
α-helix22-4625
α-helix47-515
α-helix58-592
α-helix61-7717
β-strand87-971162
β-strand100-102363
α-helix108-1103
α-helix111-1188
α-helix126-1305
β-strand138-1471062
β-strand150-1591062
α-helix1621
β-strand163164
α-helix1641
β-strand172164
β-strand176-177259
α-helix179-19921
α-helix204-2063
β-strand219165
α-helix220-23314
β-strand236-238362
α-helix2391
β-strand243-247562
β-strand248166
β-strand251166
β-strand266-268362
α-helix271-2799
β-strand310165
β-strand316-3251062
β-strand333-339763
α-helix344-3463
β-strand359-362467
α-helix373-38513
β-strand390-391267
α-helix393-3953
α-helix3991
α-helix4011
α-helix406-42823
β-strand432-434367
α-helix435-4373
β-strand438-444763
α-helix445-4506
α-helix456-4583
β-strand461177
α-helix467-4704
β-strand475168
β-strand480168
α-helix482-49110
β-strand496-497263
β-strand500-5101162
β-strand521-526662
β-strand537-539359
α-helix548-56114
β-strand569-571362
α-helix572-5765
Chain 5: 2 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix43-9654
α-helix101-11111
Chain 8: 8 helices, 6 β-strands
ElementResiduesLengthSheet
β-strand10-18955
α-helix26-283
α-helix29-357
α-helix39-4911
β-strand57-65955
β-strand70-74555
α-helix77-848
α-helix87-893
β-strand103-104256
α-helix106-11611
α-helix125-13915
β-strand142-143256
β-strand146156
α-helix148-15710
Chain 9: 4 helices, 2 β-strands
ElementResiduesLengthSheet
α-helix12-3322
α-helix53-6311
β-strand84-85258
α-helix91-11020
α-helix139-15113
β-strand167-169359
Chain a: 4 helices, 7 β-strands
ElementResiduesLengthSheet
β-strand72-74360
α-helix75-817
α-helix84-929
β-strand99-1002118
β-strand101-103361
α-helix104-1074
β-strand111-113360
β-strand124-127461
β-strand129-130260
α-helix132-14110
β-strand144-147461
Chain A: 10 helices, 15 β-strands
ElementResiduesLengthSheet
α-helix3-53
α-helix6-94
α-helix10-123
α-helix14-163
α-helix29-313
α-helix34-385
β-strand40-49101
β-strand58-6471
β-strand71-7771
α-helix781
β-strand7912
β-strand8313
β-strand87-9151
β-strand101-10331
α-helix104-1063
β-strand112-11431
β-strand11614
β-strand12614
β-strand134-14071
β-strand145-14951
β-strand155-15951
β-strand163-16641
β-strand16912
α-helix174-1763
α-helix182-1909
Chain b: 30 helices, 13 β-strands
ElementResiduesLengthSheet
α-helix14-2815
α-helix39-6729
α-helix76-8611
α-helix88-11629
α-helix122-14120
α-helix144-15714
β-strand169-174675
α-helix180-1878
β-strand205-210675
β-strand215-220675
α-helix234-24512
β-strand249-255775
α-helix264-27310
α-helix275-2773
β-strand282-288775
α-helix295-2973
α-helix300-31112
β-strand316-319475
α-helix325-34824
α-helix355-3617
β-strand364153
α-helix380-3845
α-helix385-3884
α-helix396-3983
α-helix399-4068
α-helix416-4194
α-helix425-4273
α-helix431-4333
β-strand435-436273
β-strand439-440273
α-helix449-46618
β-strand478176
β-strand481176
α-helix483-51028
α-helix517-5204
β-strand525-527310
α-helix528-53811
α-helix543-55513
α-helix562-5676
α-helix575-5773
β-strand595177
α-helix596-60914
α-helix611-6155
Chain B: 23 helices, 19 β-strands
ElementResiduesLengthSheet
α-helix9-102
α-helix14-163
α-helix32-354
α-helix40-412
β-strand42-43269
β-strand45-601670
β-strand70-801170
α-helix82-832
β-strand84-951271
β-strand98-106971
α-helix112-1154
α-helix116-1183
α-helix122-1243
α-helix131-1344
α-helix135-1373
α-helix139-1413
α-helix144-15411
β-strand157-163771
α-helix166-1683
β-strand178-182571
β-strand183-184269
α-helix188-19811
β-strand202-203271
α-helix205-2073
β-strand214-220770
α-helix221-2222
β-strand223-227572
α-helix229-2335
α-helix235-2395
β-strand268-271472
β-strand274-2861370
β-strand299173
α-helix3071
β-strand311174
β-strand315174
β-strand321-325570
β-strand335-340670
α-helix348-3503
α-helix352-3543
β-strand356-359470
α-helix373-3808
α-helix384-3863

48 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
60S ribosomal protein L2-AAprotein254Saccharomyces cerevisiae BY4741P0CX45 (AlphaFold model)
25S rRNA1RNA3396Saccharomyces cerevisiae BY4741
5.8S rRNA2RNA158Saccharomyces cerevisiae BY4741
5S rRNA3RNA121Saccharomyces cerevisiae BY4741
rRNA-processing protein5protein120Saccharomyces cerevisiae BY4741P53188 (AlphaFold model)
ITS26RNA87Saccharomyces cerevisiae BY4741
60S ribosomal protein L12-A8protein165Saccharomyces cerevisiae BY4741P0CX53 (AlphaFold model)
Ribosome biogenesis protein ALB19protein175Saccharomyces cerevisiae BY4741P47019 (AlphaFold model)
60S ribosomal protein L3Bprotein387Saccharomyces cerevisiae BY4741P14126
60S ribosomal protein L4-ACprotein362Saccharomyces cerevisiae BY4741P10664
60S ribosomal protein L5Dprotein297Saccharomyces cerevisiae BY4741P26321
60S ribosomal protein L6-AEprotein176Saccharomyces cerevisiae BY4741Q02326

48 more molecules are not listed.

Sequence of entity 1 (A), FASTA
>7V08_1 60S ribosomal protein L2-A (chains A)
MGRVIRNQRKGAGSIFTSHTRLRQGAAKLRTLDYAERHGYIRGIVKQIVHDSGRGAPLAK
VVFRDPYKYRLREEIFIANEGVHTGQFIYAGKKASLNVGNVLPLGSVPEGTIVSNVEEKP
GDRGALARASGNYVIIIGHNPDENKTRVRLPSGAKKVISSDARGVIGVIAGGGRVDKPLL
KAGRAFHKYRLKRNSWPKTRGVAMNPVDHPHGGGNHQHIGKASTISRGAVSGQKAGLIAA
RRTGLLRGSQKTQD
Sequence of entity 2 (1), FASTA
>7V08_2 25S rRNA (chains 1)
GUUUGACCUCAAAUCAGGUAGGAGUACCCGCUGAACUUAAGCAUAUCAAUAAGCGGAGGA
AAAGAAACCAACCGGGAUUGCCUUAGUAACGGCGAGUGAAGCGGCAAAAGCUCAAAUUUG
AAAUCUGGUACCUUCGGUGCCCGAGUUGUAAUUUGGAGAGGGCAACUUUGGGGCCGUUCC
UUGUCUAUGUUCCUUGGAACAGGACGUCAUAGAGGGUGAGAAUCCCGUGUGGCGAGGAGU
GCGGUUCUUUGUAAAGUGCCUUCGAAGAGUCGAGUUGUUUGGGAAUGCAGCUCUAAGUGG
GUGGUAAAUUCCAUCUAAAGCUAAAUAUUGGCGAGAGACCGAUAGCGAACAAGUACAGUG
AUGGAAAGAUGAAAAGAACUUUGAAAAGAGAGUGAAAAAGUACGUGAAAUUGUUGAAAGG
GAAGGGCAUUUGAUCAGACAUGGUGUUUUGUGCCCUCUGCUCCUUGUGGGUAGGGGAAUC
UCGCAUUUCACUGGGCCAGCAUCAGUUUUGGUGGCAGGAUAAAUCCAUAGGAAUGUAGCU
UGCCUCGGUAAGUAUUAUAGCCUGUGGGAAUACUGCCAGCUGGGACUGAGGACUGCGACG
UAAGUCAAGGAUGCUGGCAUAAUGGUUAUAUGCCGCCCGUCUUGAAACACGGACCAAGGA
GUCUAACGUCUAUGCGAGUGUUUGGGUGUAAAACCCAUACGCGUAAUGAAAGUGAACGUA
GGUUGGGGCCUCGCAAGAGGUGCACAAUCGACCGAUCCUGAUGUCUUCGGAUGGAUUUGA
GUAAGAGCAUAGCUGUUGGGACCCGAAAGAUGGUGAACUAUGCCUGAAUAGGGUGAAGCC
AGAGGAAACUCUGGUGGAGGCUCGUAGCGGUUCUGACGUGCAAAUCGAUCGUCGAAUUUG
GGUAUAGGGGCGAAAGACUAAUCGAACCAUCUAGUAGCUGGUUCCUGCCGAAGUUUCCCU
CAGGAUAGCAGAAGCUCGUAUCAGUUUUAUGAGGUAAAGCGAAUGAUUAGAGGUUCCGGG
GUCGAAAUGACCUUGACCUAUUCUCAAACUUUAAAUAUGUAAGAAGUCCUUGUUACUUAA
UUGAACGUGGACAUUUGAAUGAAGAGCUUUUAGUGGGCCAUUUUUGGUAAGCAGAACUGG
CGAUGCGGGAUGAACCGAACGUAGAGUUAAGGUGCCGGAAUACACGCUCAUCAGACACCA
CAAAAGGUGUUAGUUCAUCUAGACAGCCGGACGGUGGCCAUGGAAGUCGGAAUCCGCUAA
GGAGUGUGUAACAACUCACCGGCCGAAUGAACUAGCCCUGAAAAUGGAUGGCGCUCAAGC
GUGUUACCUAUACUCUACCGUCAGGGUUGAUAUGAUGCCCUGACGAGUAGGCAGGCGUGG
AGGUCAGUGACGAAGCCUAGACCGUAAGGUCGGGUCGAACGGCCUCUAGUGCAGAUCUUG
GUGGUAGUAGCAAAUAUUCAAAUGAGAACUUUGAAGACUGAAGUGGGGAAAGGUUCCACG
UCAACAGCAGUUGGACGUGGGUUAGUCGAUCCUAAGAGAUGGGGAAGCUCCGUUUCAAAG
GCCUGAUUUUAUGCAGGCCACCAUCGAAAGGGAAUCCGGUUAAGAUUCCGGAACCUGGAU
AUGGAUUCUUCACGGUAACGUAACUGAAUGUGGAGACGUCGGCGCGAGCCCUGGGAGGAG
UUAUCUUUUCUUCUUAACAGCUUAUCACCCCGGAAUUGGUUUAUCCGGAGAUGGGGUCUU
AUGGCUGGAAGAGGCCAGCACCUUUGCUGGCUCCGGUGCGCUUGUGACGGCCCGUGAAAA
UCCACAGGAAGGAAUAGUUUUCAUGCCAGGUCGUACUGAUAACCGCAGCAGGUCUCCAAG
GUGAACAGCCUCUAGUUGAUAGAAUAAUGUAGAUAAGGGAAGUCGGCAAAAUAGAUCCGU
AACUUCGGGAUAAGGAUUGGCUCUAAGGGUCGGGUAGUGAGGGCCUUGGUCAGACGCAGC
GGGCGUGCUUGUGGACUGCUUGGUGGGGCUUGCUCUGCUAGGCGGACUACUUGCGUGCCU
UGUUGUAGACGGCCUUGGUAGGUCUCUUGUAGACCGUCGCUUGCUACAAUUAACGAUCAA
CUUAGAACUGGUACGGACAAGGGGAAUCUGACUGUCUAAUUAAAACAUAGCAUUGCGAUG
GUCAGAAAGUGAUGUUGACGCAAUGUGAUUUCUGCCCAGUGCUCUGAAUGUCAAAGUGAA
GAAAUUCAACCAAGCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAGCCAA
AUGCCUCGUCAUCUAAUUAGUGACGCGCAUGAAUGGAUUAACGAGAUUCCCACUGUCCCU
AUCUACUAUCUAGCGAAACCACAGCCAAGGGAACGGGCUUGGCAGAAUCAGCGGGGAAAG
AAGACCCUGUUGAGCUUGACUCUAGUUUGACAUUGUGAAGAGACAUAGAGGGUGUAGAAU
AAGUGGGAGCUUCGGCGCCAGUGAAAUACCACUACCUUUAUAGUUUCUUUACUUAUUCAA
UGAAGCGGAGCUGGAAUUCAUUUUCCACGUUCUAGCAUUCAAGGUCCCAUUCGGGGCUGA
UCCGGGUUGAAGACAUUGUCAGGUGGGGAGUUUGGCUGGGGCGGCACAUCUGUUAAACGA
UAACGCAGAUGUCCUAAGGGGGGCUCAUGGAGAACAGAAAUCUCCAGUAGAACAAAAGGG
UAAAAGCCCCCUUGAUUUUGAUUUUCAGUGUGAAUACAAACCAUGAAAGUGUGGCCUAUC
GAUCCUUUAGUCCCUCGGAAUUUGAGGCUAGAGGUGCCAGAAAAGUUACCACAGGGAUAA
CUGGCUUGUGGCAGUCAAGCGUUCAUAGCGACAUUGCUUUUUGAUUCUUCGAUGUCGGCU
CUUCCUAUCAUACCGAAGCAGAAUUCGGUAAGCGUUGGAUUGUUCACCCACUAAUAGGGA
ACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUACUGAUGAAUGUUA
CCGCAAUAGUAAUUGAACUUAGUACGAGAGGAACAGUUCAUUCGGAUAAUUGGUUUUUGC
GGCUGUCUGAUCAGGCAUUGCCGCGAAGCUACCAUCCGCUGGAUUAUGGCUGAACGCCUC
UAAGUCAGAAUCCAUGCUAGAACGCGGUGAUUUCUUUGCUCCACACAAUAUAGAUGGAUA
CGAAUAAGGCGUCCUUGUGGCGUCGCUGAACCAUAGCAGGCUAGCAACGGUGCACUUGGC
GGAAAGGCCUUGGGUGCUUGCUGGCGAAUUGCAAUGUCAUUUUGCGUGGGGAUAAAUCAU
UUGUAUACGACUUAGAUGUACAACGGGGUAUUGUAAGCAGUAGAGUAGCCUUGUUGUUAC
GAUCUGCUGAGAUUAAGCCUUUGUUGUCUGAUUUGU
Sequence of entity 3 (2), FASTA
>7V08_3 5.8S rRNA (chains 2)
AAACUUUCAACAACGGAUCUCUUGGUUCUCGCAUCGAUGAAGAACGCAGCGAAAUGCGAU
ACGUAAUGUGAAUUGCAGAAUUCCGUGAAUCAUCGAAUCUUUGAACGCACAUUGCGCCCC
UUGGUAUUCCAGGGGGCAUGCCUGUUUGAGCGUCAUUU
Sequence of entity 4 (3), FASTA
>7V08_4 5S rRNA (chains 3)
GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACUGUAGUUAAGCUG
GUAAGAGCCUGACCGAGUAGUGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAAUC
U
Sequence of entity 5 (5), FASTA
>7V08_5 rRNA-processing protein (chains 5)
MVNETGESQKAAKGTPVSGKVWKAEKTPLRAKSRVVKNKKLTSWELKKQKRLEDKQFKER
LKALKDEKEEARQAKITMLKERREKKEENERYERLAAKMHAKKVERMRRREKRNKALKER
Sequence of entity 6 (6), FASTA
>7V08_6 ITS2 (chains 6)
CCUUCUCAAACAUUCUGUUUGGUAGUGAGUGAUACUCUUUGGAGUUAACUUGAAAUUGCU
GGCCUUAAAGCGAACAAUGUUCUUAAA
Sequence of entity 7 (8), FASTA
>7V08_7 60S ribosomal protein L12-A (chains 8)
MPPKFDPNEVKYLYLRAVGGEVGASAALAPKIGPLGLSPKKVGEDIAKATKEFKGIKVTV
QLKIQNRQAAASVVPSASSLVITALKEPPRDRKKDKNVKHSGNIQLDEIIEIARQMRDKS
FGRTLASVTKEILGTAQSVGCRVDFKNPHDIIEGINAGEIEIPEN
Sequence of entity 8 (9), FASTA
>7V08_8 Ribosome biogenesis protein ALB1 (chains 9)
MPSKNSINRPKLTSNLHHKVHSLNKKRAQRERAGLLKPARSSVNSKSGEIKSVALDLYFQ
NKKNESQNSTAVTLQNASSSPASITTRTLSKKRAKKIERNLKYATQRKLLVDASAKLEDE
MDIDLDGGKKVKENEKKSSLTLVKEALWSVIDDTASQGLIIENGQGTTLGGPFFP
Sequence of entity 9 (B), FASTA
>7V08_9 60S ribosomal protein L3 (chains B)
MSHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDL
DRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYK
NWYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAE
IQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPR
KTHRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDR
TKKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWID
TASKFGKGRFQTPAEKHAFMGTLKKDL
Sequence of entity 10 (C), FASTA
>7V08_10 60S ribosomal protein L4-A (chains C)
MSRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQT
SAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRY
ATASAIAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLK
VLKSKKLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAP
GAHLGRFVIWTEAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIR
PAGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKPAAVFTETLK
HD
Sequence of entity 11 (D), FASTA
>7V08_11 60S ribosomal protein L5 (chains D)
MAFQKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDI
ICQIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYATGLLIARRTLQKLGLDETYK
GVEEVEGEYELTEAVEDGPRPFKVFLDIGLQRTTTGARVFGALKGASDGGLYVPHSENRF
PGWDFETEEIDPELLRSYIFGGHVSQYMEELADDDEERFSELFKGYLADDIDADSLEDIY
TSAHEAIRADPAFKPTEKKFTKEQYAAESKKYRQTKLSKEERAARVAAKIAALAGQQ
Sequence of entity 12 (E), FASTA
>7V08_12 60S ribosomal protein L6-A (chains E)
MSAQKAPKWYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLED
NTLLISGPFKVNGVPLRRVNARYVIATSTKVSVEGVNVEKFNVEYFAKEKLTKKEKKEAN
LFPEQQNKEIKAERVEDQKVVDKALIAEIKKTPLLKQYLSASFSLKNGDKPHMLKF

Ligands and cofactors

IDNameFormulaCopies
MGMagnesium ionMg81
B3P2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-pr…C11 H26 N2 O63
ZNZinc ionZn5
GDPGuanosine-5'-diphosphateC10 H15 N5 O11 P22

Water and common crystallization additives (K) are not listed.

Primary citation

rRNA methylation by Spb1 regulates the GTPase activity of Nog2 during 60S ribosomal subunit assembly. Sekulski, K., Cruz, V.E., Weirich, C.S. et al. Nat Commun (2023) 14:1207-1207. DOI 10.1038/s41467-023-36867-5 · PubMed

Other PDB entries of the same protein (UniProt P0CX45 (AlphaFold model), which also has an AlphaFold model), best resolution first:

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